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protein identification problem

From: Ken I Fukuda <fukuda-cbrc@aist.go.jp>
Date: Wed, 29 Jun 2005 11:37:59 -0400
To: public-semweb-lifesci@w3.org
Message-Id: <20050628132552.35A5.FUKUDA-CBRC@aist.go.jp>

Hi all,

In the ISMB Semantic web for Life Science BOF,
an issue was raised about the ambiguity of how people
refer to a protein in the literature.

For example, let's say, you find a description such as
"JNK activates JUN" but acctually this "JNK" stands for
a bunch of proteins ("concrete entities") and JUN
also stands for a set of proteins.

This isssue is known as the "generic entitity" problem.
If you read the literature, you typically encounter these
"generic protein" names.
And there should be a mechanism that tells you how many
proteins you have for each generic name.

An ontology for generic/concrete protein names, called
"MoleculeRole Ontology" is available from
Actually, it is a DAG structured controled vocabulary (CV).
The current version covers about 4400 Uniprot IDs which means
that the CV defines generic/concrete protein relations for
more than 4400 concrete proteins.

The CV is available in OBO format (Gene Ontology native format).

There are some OBO->OWL converters, but some argued they didn't
fit their needs. It would be nice to know how people like to
convert an OBO ontology into an OWL file.


Ken Ichiro Fukuda, Ph.D.
Computational Biology Research Center (CBRC)
National Institute of 
Advanced Industrial Science and Technology (AIST)
AIST Tokyo Waterfront Bio-IT Research Bldg. 10F
2-42 Aomi, Koutou-ku, Tokyo 135-0064 JAPAN
Phone: +81-3-3599-8049  FAX: +81-3-3599-8081
fukuda-cbrc@aist.go.jp / fukuda_cbrc@yahoo.co.jp
     - http://www.cbrc.jp/~fukuda/index.html
- INOH Pathway Database Project -
     - Integrating Network Objects with Hierarchies
     - http://www.inoh.org
Received on Thursday, 30 June 2005 02:20:34 UTC

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